1i34
From Proteopedia
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SOLUTION DNA QUADRUPLEX WITH DOUBLE CHAIN REVERSAL LOOP AND TWO DIAGONAL LOOPS CONNECTING GGGG TETRADS FLANKED BY G-(T-T) TRIAD AND T-T-T TRIPLE
Overview
The architecture of G-G-G-G tetrad-aligned DNA quadruplexes in monovalent, cation solution is dependent on the directionality of the four strands, which in turn are defined by loop connectivities and the guanine syn/anti, distribution along individual strands and within individual G-G-G-G, tetrads. The smallest unimolecular G-quadruplex belongs to the, d(G2NnG2NnG2NnG2) family, which has the potential to form two stacked, G-tetrads linked by Nn loop connectivities. Previous studies have focused, on the thrombin-binding DNA aptamer d(G2T2G2TGTG2T2G2), where Nn was T2, for the first and third connecting loops and TGT for the middle connecting, loop. This DNA aptamer in K(+) cation solution forms a unimolecular, G-quadruplex stabilized by two stacked G(syn)-G(anti)-G(syn)-G(anti), tetrads, adjacent strands which are antiparallel to each other and, edge-wise connecting T2, TGT and T2 loops. We now report on the NMR-based, solution structure of the d(G2T4G2CAG2GT4G2T) sequence, which differs from, the thrombin-binding DNA aptamer sequence in having longer first (T4) and, third (GT4) loops and a shorter (CA) middle loop. This d(G2T4G2CAG2GT4G2T), sequence in Na(+) cation solution forms a unimolecular G-quadruplex, stabilized by two stacked G(syn)-G(syn)-G(anti)-G(anti) tetrads, adjacent, strands which have one parallel and one antiparallel neighbors and, distinct non-edge-wise loop connectivities. Specifically, the longer first, (T4) and third (GT4) loops are of the diagonal type while the shorter, middle loop is of the double chain reversal type. In addition, the pair of, stacked G-G-G-G tetrads are flanked on one side by a G-(T-T) triad and on, the other side by a T-T-T triple. The distinct differences in strand, directionalities, loop connectivities and syn/anti distribution within, G-G-G-G tetrads between the thrombin-binding DNA aptamer, d(G2T2G2TGTG2T2G2) quadruplex reported previously, and the, d(G2T4G2CAG2GT4G2T) quadruplex reported here, reinforces the polymorphic, nature of higher-order DNA architectures. Further, these two small, unimolecular G-quadruplexes, which are distinct from each other and from, parallel-stranded G-quadruplexes, provide novel targets for ligand, recognition. Our results demonstrate that the double chain reversal loop, connectivity identified previously by our laboratory within the, Tetrahymena telomere d(T2G4)4 quadruplex, is a robust folding topology, since it has now also been observed within the d(G2T4G2CAG2GT4G2T), quadruplex. The identification of a G-(T-T) triad and a T-T-T triple, expands on the available recognition alignments for base triads and, triples.
About this Structure
1I34 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
A double chain reversal loop and two diagonal loops define the architecture of a unimolecular DNA quadruplex containing a pair of stacked G(syn)-G(syn)-G(anti)-G(anti) tetrads flanked by a G-(T-T) Triad and a T-T-T triple., Kuryavyi V, Majumdar A, Shallop A, Chernichenko N, Skripkin E, Jones R, Patel DJ, J Mol Biol. 2001 Jun 29;310(1):181-94. PMID:11419945
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